My Jalapeno has the following three yellow spots on it, is this maybe a sign of overfertilizing? Other plants don't have such spots anywhere though but some of them have distorted leaves as I mentioned in another post.
However, some other issues begin as yellow spots that later turn brown or black. Bacterial Leaf Spot (BLS) is one of them. In case it is early BLS, I'd suggest moving the plant away from any others. Wear gloves and wash your hands thoroughly whenever you handle this plant. Don't handle other plants until you've washed your hands well, to help prevent the spread of it. That said, I hope it's just a magnesium deficiency - spraying some epsom salt on the leaves is all you have to do for that, or get a fertilizer that has more magnesium in it than what you are currently using.